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Programme: This Project is not associated with a Programme
SEEK ID: https://fairdomhub.org/projects/156
Public web page: Not specified
Organisms: No Organisms specified
FAIRDOM PALs: No PALs for this Project
Project created: 29th Jul 2019
Related items
- People (4)
- Institutions (1)
- Investigations (0+4)
- Studies (1+1)
- Assays (4+2)
- Data files (1+1)
- SOPs (2)
- Documents (8)
Projects: Simulation Foundries
Institutions: University of Stuttgart

Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.
Projects: Simulation Foundries
Institutions: University of Stuttgart
Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.
Person responsible: Gudrun Gygli
Snapshots: Snapshot 1, Snapshot 2
Investigation: 1 hidden item
Assays: Analysis Version 1.5, Preparation, Results, Simulation Version 1.5
Here would be the results from the Analysis part of the Simulation foundry. For the newest version, which was improved based on reviewers comments to represent best practices, of the Simulation Foundry for Methanol-Water mixtures no such results exist yet.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
This is the simulation part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name.
Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Assay type: Molecular Dynamics
Technology type: All-Atom
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
SOPs: SIMULATIONS_V1.5
Data files: No Data files
This is the analysis part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name.
Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
Models: No Models
SOPs: ANALYSIS_1.5
Data files: No Data files
Preparation needed to use Simulation Foundry, Version 1.5.
Please read the manual before working with this Simulation Foundry.
Pay careful attention to the installation instructions.
Note the known issues.
Submitter: Gudrun Gygli
Assay type: Instructions
Technology type: Technical Computer Installation
Snapshots: No snapshots
Investigation: 1 hidden item
Study: Simulation Foundry for Methanol-Water Mixtures
Organisms: No organisms
SOPs: No SOPs
Data files: Installation Instructions
Follow the instructions in this file to get the necessary software packages to run the Simulation Foundry Version 1.5.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Preparation
Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry.
Make sure you followed "Preparations" instructions!
Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Simulation Version 1.5
Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry.
Make sure you followed "Preparations" instructions!
Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Analysis Version 1.5
Scripts and Input Files for Simulation V1.5
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Simulation Version 1.5
Overview of the results obtained from the Simulation Foundry.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Overview of the quality control checks obtained from the Simulation Foundry.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This is a list of errors that can be produced if the Simulation Foundry is not used correctly - the messages are cryptic, hopefully the file is helpful to some.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Preparation
Manual to Simulation Foundry Version 1.5.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Preparation
Scripts and Input Files for Analysis V1.5
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Analysis Version 1.5
OPLSAA force field used by GROMACS on the BINAC Supercomputer (chem/gromacs/5.1.4-gnu-4.9, https://wiki.bwhpc.de/e/Category:BwForCluster_BinAC )
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Preparation
Screenshot of the directory structure required for the Simulation Foundry.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: 1 hidden item
Studies: Simulation Foundry for Methanol-Water Mixtures
Assays: Preparation